A Healthy Gut Is the Hidden Key to Weight Loss | Chris Kresser
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A Healthy Gut Is the Hidden Key to Weight Loss

by Chris Kresser

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In a previous article in this series on diabesity and metabolic syndrome I briefly mentioned the role of gut health in obesity and diabetes. I’d like to go into more detail on that subject here, especially since it’s not a very well known relationship.

Our gut is home to approximately 100,000,000,000,000 (100 trillion) microorganisms. That’s such a big number our human brains can’t really comprehend it. One trillion dollar bills laid end-to-end would stretch from the earth to the sun – and back – with a lot of miles to spare. Do that 100 times and you start to get at least a vague idea of how much 100 trillion is.

The human gut contains 10 times more bacteria than all the human cells in the entire body, with over 400 known diverse bacterial species. In fact, you could say that we’re more bacterial than we are human. Think about that one for a minute.

We’ve only recently begun to understand the extent of the gut flora’s role in human health and disease. Among other things, the gut flora promotes normal gastrointestinal function, provides protection from infection, regulates metabolism and comprises more than 75% of our immune system. Dysregulated gut flora has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s, inflammatory bowel disease and type 1 diabetes.

Recent research has shown that the gut flora, and the health of the gut in general, also play a significant role in both obesity and diabetes. I’ve seen this anecdotally in my practice as well. Nearly every patient I treat with a blood sugar issue also has a leaky gut, a gut infection, or some other chronic inflammatory gut condition.

We now know that the composition of the organisms living in your gut determines – to some extent, at least – how your body stores the food you eat, how easy (or hard) it is for you to lose weight, and how well your metabolism functions. Let’s take a closer look at the mechanisms involved.

Intestinal Bacteria Drive Obesity and Metabolic Disease

A study published this year in Science magazine found that mice without a protein known as toll-like receptor 5 (TLR5) in their gut gain excessive weight and develop full-blown diabetes and fatty liver disease when fed a high-fat diet. If we think of the gut flora as a community, TLR5 is like a neighborhood police force that can keep the houligans in check. Without TLR5, bad bacteria can get out of control.

The study authors found that these bad bacteria caused a low-grade inflammation in the mice, which caused them to eat more and develop insulin resistance. They also found that treating these mice with strong antibiotics (enough to kill most of the bacteria in the gut) reduced their metabolic abnormalities.

But the most interesting part of this study is what happened when the researchers transferred the gut flora from the TLR5-deficient overweight mice into the guts of skinny mice: the skinny mice immediately started eating more and eventually developed the same metabolic abnormalities the overweight mice had. In other words, obesity and diabetes were “transferred” from one group of mice to the other simply by changing their gut flora (as shown in the image below).


Other studies have shown that the composition of the gut flora differs in people who are obese and diabetic, and people who are normal weight with no metabolic irregularities.

One possible mechanism for how changes in the gut flora cause diabesity is that different species of bacteria seem to have different effects on appetite and metabolism. In the study on TLR5 deficient mice I mentioned above, the mice with too much bad bacteria in their guts experienced an increase in appetite and ate about 10 percent more food than their regular relatives. But it wasn’t just that these mice were hungrier and eating more; their metabolisms were damaged. When their food was restricted, they lost weight – but still had insulin resistance.

Other studies have shown that changes in the gut flora can increase the rate at which we absorb fatty acids and carbohydrates, and increase the storage of calories as fat. This means that someone with bad gut flora could eat the same amount of food as someone with a healthy gut, but extract more calories from it and gain more weight.

Bad bugs in the gut can even directly contribute to the metabolic syndrome by increasing the production of insulin (leading to insulin resistance), and by causing inflammation of the hypothalamus (leading to leptin resistance).

How Modern Life Screws up Our Gut and Makes Us Fat and Diabetic

What all of this research suggests is that healthy gut bacteria is crucial to maintaining normal weight and metabolism. Unfortunately, several features of the modern lifestyle directly contribute to unhealthy gut flora:

  • Antibiotics and other medications like birth control and NSAIDs
  • Diets high in refined carbohydrates, sugar and processed foods
  • Diets low in fermentable fibers
  • Dietary toxins like wheat and industrial seed oils that cause leaky gut
  • Chronic stress
  • Chronic infections

We also know that infants that aren’t breast-fed and are born to mothers with bad gut flora are more likely to develop unhealthy gut bacteria, and that these early differences in gut flora may predict overweight and obesity in the future.

It’s interesting to note that the diabesity epidemic has neatly coincided with the increasing prevalence of factors that disrupt the gut flora. I’m not suggesting that poor gut health is the single cause of obesity and diabetes, but I am suggesting that it likely plays a much larger role than most people think.

How to Maintain and Restore Healthy Gut Flora

The most obvious first step in maintaining a healthy gut is to avoid all of the things I listed above. But of course that’s not always possible, especially in the case of chronic stress and infections, and whether we were breast-fed or our mothers had healthy guts.

If you’ve been exposed to some of these factors, there are still steps you can take to restore your gut flora:


Join the conversation

  1. Something I was advised on with respect to cleansing parasites out of the intestinal track is to consume a handful of raw pumpkin seeds every am 20 minutes before anything else.

  2. Hello, i have recently started on the loette contraceptive pill but i also started drinking yakult well the cheap version pro-b. I was wondering if that affected the pill at all?

  3. Hi Chris,
    I wanted to know if you or anyone else on this thread has heard of the Plexus products ProBio5 (a probiotic) & Biocleanse. They are GREAT at helping get the gut healthy, as well as The Plexus slim. Numerous testimonies support these products. I’m sure this isn’t a place to “promote” personal websites or business but I mainly wanted to know if Chris has any insight to the research w/ Gut Health & Plexus??


    • I have started 3 weeks ago, already seeing a dramatic change in my sugar numbers… I am type two diabetic… taking triplex from plexus.

  4. I like to drink a super green powder mix,That is also great for your gut flora…It will give you a few extra servings of vegetables if you don’t get enough for the day.It is a good way to get a mixture of veggies in a powder drink mix.I have found one for only 13 bucks at Vitacost-It is Berrytastic.I am not one of these people that are going to spend 30 or 40 bucks on a protein or veggie drink mix.I think its a good way to get extra fiber and veggies and it does help out when you have to go to the restroom.

  5. Maybe somebody can give me advice:

    I can not tolerate fermented foods because of histamine intolerance. So I take a probiotic.

    I suffer from a chronic procitits. At the beginning I felt little pain and had bloody stool, higher calprotectin. Through a Paleo diet (no gluten, low histamine, diary and egg free) I got rid of many symptoms like the bloody stool and most of the pain (was not much pain). But I still suffer from irregular motility and mood and energy swings which correlate with my bowel movements. This means:
    I am often constipated for 2-3 days. Then I have either normal motility like I always had (2-3 per day) or I have one movement per day. When having my old motility back, I feel good energy. But the most time I feel like a little subdepressive and low energy…

    When I had acute proctitis the first and only time, I could not tolerate anything but rice and potatoes. Sugar and diary gave me massive mood swings (anxiety). Had to eat rice and potatoes for a week with a probiotic to get normal again…

    Since I suffer from proctitis I cannot tolerate any Gluten, or FOODMAPS. Foodmaps give me heavy brainfog and constipation (tried inulin)

    I tried Bimuno (GOS) which my gut tolerated well, but I react allergic to it (I react to many things :-/)

    So I ask myself if could use Lactulose as a prebiotic for a longer time. Is this an good alternative to inulin or FOS?

    In my probiotic is FOS, but the bacteria eat it all up during the preactivation- phase (has to be diluted in water 25 minutes before drinking)

    Or should I start with tiny amounts of FOS?! But even a tiny capsule of Inulin gaves me heavy brain fog for days last time I tried it. I have no idea where to go with there issues. There´s no Chris Kresser in Germany…:-/

    Can anybody help me with this?

    • I wouldn’t worry about taking a prebiotic, I don’t think they make a lot of sense — if you think about it prebiotics are designed to “feed” the probiotics in your intestinal track… but you’re also going to be “feeding” the BAD bacteria along with the good bacteria! It also doesn’t make sense to activate the probiotic bacteria BEFORE you ingest them — how will they get through your stomach acid alive? They are better left inactive until they get to the small and large intestine where they naturally thrive…. I would suggest that you just take a good probiotic. The strain Lactobacillus bulgaricus, strain LB-51 in the Natren line of probiotics is excellent for gut motility and improving constipation. I like their probiotics because they offer a powdered form which really allows you to start at a low dose (1/8 of a teaspoon or so..) and work up to a higher dose, it’s great for those of us with sensitivities!

      • Thank you for your reply.

        Bur I think you are wrong.

        Prebiotics feed mainly the good bacteria. And the probiotic which I take works even better than older ones because of the preactivation.

        L. Bulgaricus is histamine building and I am intolerant to histamine. So this would not be a good idea.

        As your info is exactly the opposite if what I learned: where do you have this information from?

        Thank you

        • I’ve read numerous studies about prebiotics because it just didn’t seem to make biological sense to me. At it’s very basic a prebiotic is something that our body doesn’t digest well (so it passes through the small intestine generally untouched) and our bacteria in our large intestine break it down instead. So, by their very nature, they are apt to disturb our digestion since they are non-digestible items…. and I think they do, they’ve shown that we don’t tolerate them well in large doses, so in small doses we just don’t notice what they are doing to our body, perhaps… ?

          I just don’t see how the good bacteria are more likely to utilize it? Bacteria are opportunistic organisms, I’m extrapolating here but I think that any of them would be able to use a prebiotic as an energy source. And I’ve seen studies where prebiotics have worsened pathogenic infections so obviously pathogenic bacteria are using these as well.

          Here’s a few studies on this topic that may interest you:



          I don’t know about histamine, so I’m sorry I can’t really comment further on that.

          • Hello again,

            thank you for your answer again.

            I don´t think that they can “eat” all prebiotics. I also read many studies and in most cases there was a specific class or sometimes even just a specific bacterium which proliferates most in the prebiotic group. At the same time in most cases, the overall count of bacteria was not influenced. So, there must have been a shift in population towards the specific bacteria which could eat the prebiotic.

            I only read one study where lactulose also enhanced a specific species of clostridia. But in most studies they found lactulose to enhance bifido bacteria.

            I found the same for Inulin, FOS and other GOS than Lactulose…

            Maybe the infection is the variable, which counts, because in the most studies I read about, there participants were healthy.

            But I don´t think that I have an infection (never found something like that in many diagnostic processes.

            And I also don´t think prebiotics are harmful for our digestion, as they lead to more bifidobacteria which is associated with many health benefits…


        • What you might try is a probiotic that also has an anti fungal, and chitonase to break the exoskeleton of bad bacteria. You want to fee the good while killing the bad. I take this with a magnesium supplement (Bio Cleanse) which flushes out the bad ensuring it is not reabsorbed into your system. Magnesium also oxygenates the body. It’s working for me. 🙂

    • HI there,

      does your probiotic contain the ingredient Chitosasane?? That ingredient is very beneficial in killing the bad bacteria in your gut that may cause so many symptoms. There are so many probiotics out there but you have to pay careful attention to see if they are just replenishing the good and doing nothing with the bad – if so you’re not getting the full benefits of a probiotic.

    • Hi,

      regarding your mood swings, you probably have a sensitivity to “free glutamic acid”, Chris has another post about this


      I have this myself, but it took years to find out that specific foods trigger neurological symptoms, cause it’s kind of all foods 🙁

      here’s a list of foods to avoid, if this is the case


      Did you consider getting a fecal transplant (Stuhltransplantation)?

      I also live in (the south of) Germany by the way 🙂

  6. Ugh. This really intrigued me, and then nothing. It felt like one of those scam emails that tells me everything I want to hear and promises a cure…once I click on a link and pay $49.95.

  7. Thank you.

    I’d like to know how to get more TLR5, where it comes from, or how it is made. I can’t learn a new word and not know what it’s all about. I’m guessing it has something to do with healthy habits and the avoidance of unhealthy habits.

  8. I’ve been reading about probiotics and insulin resistance and obesity, etc. I have been taking a good quality probiotic for a few months now and have just been diagnosed with insulin resistance for which I have been placed on medication. I also have high blood pressure, high cholesterol and thyroid antibodies causing hypothyroidism. The bacteria in my probiotic are Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium Ion gum, & Saccharomyces boulardii. Maybe they are just the wrong ones!

    • It’s an issue of quality over quantity too. If your gut is unhealthy you may not be able absorb all the nutrients you are eating. I too am insulin resistant. I take a chromium supplement (other ingredients too) which helps to maintain muscle, burn fat, make your body more sensitive to insulin, reduces carb cravings (a game changer for me!). I take a probiotic to feed good bacteria. It has an anti fungal and a protein to break down fibrous foods (3products in one)! And a magnesium supplement to ensure the bad stuff is flushed out and not reabsorbed. Within 4 days me GERD was gone (still is!) and I’d had it over 30 yrs bc I didn’t want to take a protein pump inhibitor. Energy up, carb cravings decreased, making healthier voices.

      Happy 4th! 🙂

  9. Hi chris, why are we told to eat healthy grains if they are so bad for gut health, and also, what defines healthy grains?

  10. Hello Chris, you write that Diets high in refined carbohydrates, sugar and processed foods can contribute to unhealthy gut flora.
    I am trying to find the scientific research that proofs this. I can not find this in your articles. Can you help me?

  11. Why are the specific species of bacteria that benefit us (or the mice)not mentioned? When you buy probiotics, the bacteria, by name, is noted on the label. This study had to have determined the specific bacteria that were helpful, and harmful, yet not one article or web site mentions the specifics. This information, absent specifics, is pointless! Aren’t we ridicules.

  12. Does having too big a variety of foods disrupts formation of healthy gut bacteria? Should we consistently eat the same healthy foods or mix them up as much as possible? Thanks for your time! Great article.

  13. The link attached to this statement is not working, I was interested in seeing the reference for this, do you have that available by any chance? –> “Other studies have shown that the composition of the gut flora differs in people who are obese and diabetic, and people who are normal weight with no metabolic irregularities.”

  14. Hi Chris,

    I am at wits’ end. I eat mostly plants, always real food (lean meat, vegetables, fruit), I stay away from all gluten and refined sugar. I exercise 6 – 7 times a week, I meditate and practice yoga. Most people in my office refer to me as a health freak, but really I live like all people should.

    I am constipated and I find it beyond difficult to lose weight. I am starting to find out (after much research) that it may be the bacteria in my gut and the health of my gut. As a child and into my early adulthood (I am 28 now) I had severe tonsillitis and having antibiotics as the only treatment, I had it quite severe one year needing a shot of penicillin in my back and very strong antibiotics. A year after this I developed gluten intolerance. Some days I want to cry because its all too hard.. why, when I do everything right does it seem like I am punished.

    I have recently started taking a good quality probiotic.. I am wondering what else I can do? I have been to so many doctors that palm me off and tell me to increase my dietary fibre.

    I would also like to thank you for all the useful information you provide!


    • Well, in this case, the doctors can be right. Many people make the mistake of not getting enough fibers when they switch to a low carb diet. Getting more fiber will definitely help with the constipation.

    • Hi,
      I noticed what you’re eating is rather “healthy” as per what has been taught for a number of years bar 2 things you didn’t mention.
      How much water do you drink?
      And most importantly, you haven’t mentioned and fat in your diet?
      Healthy diets consist of 30% fat. Adding fat to your diet will loosen your faeces and lube them up. My mother has suffered from severe constipation for years and has finally added fats back into her diet and, literally within a week, her constipation has disappeared.

    • Far too little fat. That will make anyone constipated, as your colon needs to be ‘oiled’. Eat more oily fish, add olive oil to salads, and cook in butter (not vegetable fats). Lack of fat will be impeding weight loss as well. Simple rule of thumb; eat fat to lose fat, eat carbs to gain fat.

      Also, try taking an L-Glutamine supplement, very good for repairing damaged intestines and contributing to normal gut flora.

      Good luck 🙂

    • hey mate read you story and we have a similar problem
      ive had lots of antibiotics for tonsillitis and have a gluten problem too..i also struggle with acne and a flaby stomach dispite being fit and slim everywhere else..its definetly a lack of good flora in the gut..as of yesterday I started eating fermented sauerkraut and swallowed 15 probiotics.. I read that 1 a day is useless you should swallow 15 at once 2 times a month to flood the body….hope this helps.

  15. Hi Chris,
    Just wanted to check if you can recommend any efficient weight loss plan or anything that could assist in weight loss?
    I’ve recently being taking Garcinia but did notice much of a change.
    Also what thoughts do you have on Yakult? Does this assist in weight loss at all?
    Thank you

  16. I’m trying to find info on treating parasites naturally bc from what I have gathered so far (with a lot of methods used) is that the parasites become resilient. How do you suggest parasites are treated best?

    • Have you heard of humaworm? It is a natural parasite treatment that uses herbs. I am planning to do it again soon; although I did not get drastic results like some of the reviews online, I found that my eyes began to itch and I began sneezing more. Someone suggested to me that I may have stirred something (parasites? yeast?) up…Diatamaceous earth is another parasite cleanser; you can research it. Hope this helps.

    • After taking a yeast assessment and scoring extremely high I started taking a pro biotic (which also contains an anti fungal and a protein to break up fibrous foods so your body can absorb the nutrients you are consuming). I combine it with a magnesium supplement which works to flush out the toxins and yeast the probiotic is killing. It’s less expensive than the expensive probiotic my doctor recommended and within 4 days my acid reflex was gone. After over 30 years! While the two my dr gave me did nothing that I could notice.

      I’m not an expert, just know what’s been working for me. 🙂

  17. Help , I must be stressed , I have been like this since they told us our jobs are leaving , tests from the Dr. Concludes , I have more bad flora then good , it makes it really hard to go to work , always going to bathroom , can’t keep it in , I’m finding fluids are the best , and I’m gaining weight , probably fluid..

  18. Healthy gut flora is important. However eating less food and eliminating sugar and other offending foods/poison which for me include grains will lead to weight loss without the need for supplementation. Eating a diet rich in veggies & quality fish, meats will work for most people.

  19. What would you recommend for a type 1 diabetic with gastroparesis? In and out of the hospital with severe stomach pains for a year. Started acupuncture, juicing and removed gluten from the diet 3 weeks ago and haven’t been in the hospital since. Still underweight though and nervous to eat anything. Besides sweet potatoes, etc., what would you recommend eating/ supplementing with? I’m considering starting on l-glutamine, fish oil, magnesium and extra virgin coconut oil. Is it safe to eat grass-fed butter, beef and fish? Your FODMAP has been an excellent guide as have the 9 nutritional steps. Thank you.

  20. Would you mind recommending a specific panel that you have found to be the most advantageous for the first step in determining gut issues. Is the Genova Comprehensive Digestive Stool Analysis 2.0™ (CDSA 2.0) with Parasitology a good one?

  21. Just wondering if the admonition to avoid grains and legumes on these diets includes lentils and chickpeas, and thus that humus is also off the list.

  22. Great article. I have read many similar ones and I am interested in learning more about “good bacteria” and “gut cleansing” for purpose of detoxification. My little boy has just turned seven. He struggles with chronic constipation/diarrhea. For two years now his PCP has merely recommended Miralax to correct the constipation. My child is obese with stomach distention (pot belly). An X-ray once confirmed this boy gets very compacted. I have suggested that toxins and almost “tapeworm type of deal” (not that i think he has one but using the example to point out his increased hunger). He does not eat out of boredom, and he does not loaf, He is actually go go go! When he eats its on purpose, it’s his body seeking nutrition. I feel there is malabsorption going on here. I feel there is an overload of bad bacteria in his intestines which over whelm him and which have now lead to symptoms of ADHD, Why will no one listen to me? I don’t want to consider ADHD meds when i feel the primary problem is with his digestive tract. Can you lend some advice on gut cleaning options? I read that the leaky gut and toxin build up can become fatal. I am not willing to overlook this likely cause of his compaction, high hunger level, hyperactivity and recent ADHD diagnosis which i believe all to be due to trapped toxins.Thank you Chris!

  23. Hi – I’m always extremely heath-concious, although currently I have no health problems other than being overweight. I don’t eat sugars (including most fruits), any grains or processed foods. I’m basically following the paleo diet with lots of raw green juice (juiced myself), raw green vegetables, grass-fed meats and eggs. I do eat greek yogurt, drink kombucha and coconut water regularly. However, I take a birth control pill every day and I’m concerned about my gut flora. I don’t take any other medications, not even pain killers like Aleve. At this point, I don’t see a way around taking the birth control though, so what would be the best way to help defend my gut flora? Anything else besides yams and sweet potato? What is the best high quality pro-biotic? Thank you so much!

    • Hey Allison,

      I saw that you mentioned birth control I recently became engaged and started battling the inevitable birth control- which I really, really, really didn’t want to take due to synthetic hormones and their effects on the emotions, gut, body, and more. My future mother-in-law went with natural BC by measuring her basal temp every morning to determine when she was about to ovulate. With that said, I recently found the lady comp, which basically measure your basal temp and gives a green light if you aren’t soon to ovulate and a red light 5 days before ovulation to prevent pregnancy. It’s really amazing, and you don’t have to worry about hormones. I’m so excited that someone came along with this method and was innovative enough to come up with a ovulation predictor like lady comp. Here’s the link if you’re interested.

  24. HI Chris, PLEASE RESPOND, I NEED INFO. One of the steps you list to restore intestinal flora is Treat any intestinal pathogens (such as parasites) that may be present. 1 year ago took a course of antibiotics to kill h. pylori. I continued to have symptoms. 4 months ago I was diagnosed with celiac. (I’m not sure the diagnosis is accurate, because I have only 4 of the 5 diagnostic positives- the most important one (tissue samples) was negative.) I now follow a gluten free/milk-free diet. I continue to have symptoms, but much milder. I have always maintained a stable weight with no effort. Now, however, my weight climbs steadily without serious calorie restriction. I must eat no more than 1300 calories and exercise 90 minutes 6x/wk intensely to maintain a weight 5-8 lbs higher than I’ve been since reaching adulthood. The math doesn’t add up. My questions are:
    1. Is h.pylori considered to you a “good” or “bad” microorganism. I’ve been told it helps regulate appetite.
    2. I’ve also learned that some bacteria can actually prevent your body from using fat stores. What are they? Can I test for them?

  25. I like your article. Here’s my two cents’ worth: A couple years ago I really started noticing and having to work around a problem with wheat. If I ate wheat (especially commercial wheat), I had to spend about 3 days near a bathroom. So I began avoiding wheat in December 2011 and had improvement. In the meantime, someone said they had cured their problem (wheat? gluten? I don’t remember) by using a probiotic called Yakult, which originated in Japan. Because they used the term “cured” I thought I would look into it. I found that it is available at one store in my state (in another town), and I have been going to that town once a week anyway, so I started buying it. I decided I would give myself 6 weeks to really try it. I took the probiotic every day and tried even harder to avoid wheat – even organic wheat. I did see an improvement fairly quickly, but I also noticed that whenever I drank tap water or ate/drank foods made with tap water, my improvements went away. So I started wondering if there was something in the tap water that was killing off my good bugs. Long story short, after talking with the people who run the water works near me, I suspect that chloramine in the tap water has been killing off my good bugs. So now I avoid it by using spring water or well water from a friend’s farm. I can eat any amount of any type of wheat now without repercussions – as long as I avoid the tap water. Of course, eating more wheat is a mixed blessing. I can eat a wider variety of food; but I do need to lose some pounds, and I have to minimize wheat to make that happen. And I learned today that Obamacare is going to make obese people pay something like fifty percent more for their health insurance, so guess what’s on my agenda now! I really don’t want to ruin my gallbladder, though. I know several people who did that when they lost a lot of weight.

    The chloramine apparently was put into use by many utilities starting in 2010 in response to changes in EPA standards. It doesn’t kill germs as fast as plain chlorine, but it stays in the water pretty much permanently. It won’t gas out. Salt won’t neutralize it. It will kill your fish. It is deadly to use in kidney dialysis. It won’t boil out. If you want to remove it, you have to use at least a two-step process that involves exposing the water a long time to high quality activated charcoal, and then putting it through reverse osmosis (RO). One of the water works people I talked to mentioned that RO water is “aggressive”, in other words, it will eat up your pipes faster.

  26. Hi Chris, I recently began hearing about fecal bacteriotherapy and am very interested. I have something called Polycystic Ovarian Syndrome (PCOS) and in 2009, went off most carbs, dairy and sugar to lose weight and get healthy/relief from the PCOS. I lost 60 lbs in a year, but also ruined my gallbladder and had it removed in 2010. For a while, I maintained my weight, but beginning in 2012, the weight started to creep back on, I’m sick more often (my old habit of recurring sinus infections are back), brain fog is back, poor sleep, etc. And I don’t know what to do to fix it (I still refrain from carbs, dairy and sugar with the exception of sweet potatoes). Am I a candidate for fecal bacteriotherapy? Is there a doctor near Delaware who will perform this for me? I don’t know if I have leaky gut either … so I’m interested in fixing it all!

  27. Chris-
    My husband and I have been on the Primal diet since September. Things have been going great, but about a month ago my husband developed a skin rash that started on his belly and has spread to his chest and back. He has psoriasis, but this is different. They are red, but they do not itch. I am not sure if it has anything to do with the diet, but I was wondering if you have any thoughts about this. Recently, I read in the Personal Paleo Code that taking a Probiotic might cause a skin rash in some people. I think he started taking “Ultimate Flora: Adult Formula” by Renew Life a couple of weeks before he got the skin rash. He also eats fermented foods. In addition, we have been taking Vitamin D, Cod Liver Oil, and Magnesium (as we both got leg cramps in the night).

  28. A couple of links appear to be broken/missing:

    Other studies have shown that the composition of the gut flora differs in people who are obese and diabetic, and people who are normal weight with no metabolic irregularities.

    Other studies have shown that changes in the gut flora can increase the rate at which we absorb fatty acids and carbohydrates, and increase the storage of calories as fat.

    Can you provide the references for these two (might be the same reference)?


  29. Hi,

    I have had gut problems for the past year (diarrhea, bloating, cramps etc.), and severe mood swings and depression. I remember that I took a course of antibiotics for acne at the start of last year, could this be the cause? I have seen a few doctors, and they say it’s IBS or stress. I have ordered some “Biokult”, but are there any prebiotics that you would recommend?

  30. Hey Chris, thank you so much for this article. It’s fascinating. I am in the process of presenting an overview of the benefits of my company’s new probiotic, prebiotic and enzyme support product that was just launched at our global training conference last week and your article has given me some great clarification. I would be interested to get your perspective on our new product. I see you recommend the UK brand Biokult. Have you heard of Arbonne? We are a botanically based, Swiss formulated product line that’s vegan, gluten free and absolutely cutting edge. I’d be interested to get your perspective on our new Digestive Plus product. I am learning it’s not what you eat, it’s what your absorb and I think our product would be of benefit to your readers. http://www.arbonne.com. Thanks for all you do and the insight.

  31. A fantastic British probiotic brand is http://www.optibacprobiotics.co.uk – i have tried a few, and these products are all specifically tailored to different health conditions, so the products make you feel fantastic. Whats more their customer service is outstanding! and i think that goes an awfully long way in this day and age.

  32. You mentioned a probitoic brand here before. Which one was it that you recommended? I recall it was an English company.


  33. If that’s the only thing that can help in the short-term, sure. But I’d advise you to consider addressing the underlying mechanism of IBS, which is almost always intestinal dysbiosis and/or a chronic G.I. infection.

  34. Hey Chris,

    I have IBS, and I manage the foods I eat accordingly because I know what bothers me and what does not. The only thing that really triggers an immediate urge for a bowel release is the onset of stress usually in the form of anxiety or panic (which developed because of the IBS). So I take Immodium AD regularly to control this urge. Any problem with taking this aid? It is the only thing that works.

    • Ryan, you said you manage the foods you eat for your IBS. Have you done a completely gluten and dairy free trial, and if so, for how long? My sister-in-law suffered many years with an IBS diagnosis which turned out to be gluten, dairy and a few other foods based on testing, even though she thought she was managing her foods. She also takes certain probiotics and supplements under the guidance of the practitioner who found the problem. I know what you mean about the stress trigger, but like Chris says there are underlying problems.

  35. Kaitlyn,

    First, most people (but not all) with an unhealthy gut will have digestive symptoms of some sort. Skin problems, brain fog, behavioral and mood issues and problems with mineral and vitamin absorption are also signs.

    The best way to find out is get a comprehensive stool test that screens for pathogenic organisms and measures major species of gut flora, intestinal pH, and a number of other factors.


    Yes, I did mean that second link. I’ll fix it – and thanks for the tip.

  36. Hi Chris. How can we definitively find out if we have an unhealthy gut? What’s the first step? Is there a specific doctor we can see or is our best option an elimination diet and our own judgment? I suspect that I do have an unhealthy gut, but knowing for sure would give me greater motivation to strictly abstain from problematic foods. For example, I read on the Perfect Diet that as little as 1 milligram of gluten per day can prevent recovery from bowel disease, so it is essential that grains be eliminated entirely from the diet. I try not to let my dietary changes affect other people too much so I don’t always follow my typical dietary style in some social or family situations. However, I would NOT be lenient anymore if I knew that I had a leaky gut or some other bowel disease.

  37. It is more complicated than just replacing the gut flora. I had a colonoscopy earlier this year. I’d already switched to a primal diet a couple of months before the procedure and had my pro- and prebiotics ready for recolonization after the procedure. No real change in my health, still have high blood sugars etc.

  38. Hans:

    All of the toxins you mentioned play a significant role in dysregulating the gut flora, so yes, they have to be considered.

  39. Nice HOT new topic. I wonder if the gut flora question can be seen without considering other gut undermining forces like gluten, lectins, saponins and glycoalkaloids. Very best regards, Hans

  40. Solid science, Chris. Gut microbiota is strongly linked. Keep on getting the message out there. Let these fraud Internet gurus who push dieting hear you.

    Obesity is extremely complex. There are vast unknowns and uncertainties. Real researchers already know this and admit it. My blog discusses a lot of the same thing . Obesity is only simple and certain to the $ 100 billion a year dieting industry which rests precariously on false assumptions and false promises .

    Also ,please look into Urgelt from youtube. He says a lot of what you say too. That man is very intelligent and has a lot to say on obesity :))

    Take care,


  41. Good posts!

    What are your thoughts on drinking chemically treated municipal water? Does chlorine etc have an effect on gut flora? Should we be using appropriate filters? Or is this a non issue.


  42. Also, Chris, do you agree with everything on those perfecthealthdiet.com links? Because some claims in them were reaallly not science-based, and I know you want to structure your posts according to the best evidence.

  43. @Chris
    We do have a progressive GP. Too bad the NHS isn’t as progressive. He’ll have to see a private doctor to see get something done about the problem.

  44. Hi Chris,

    Thanks for another excellent post. This is a subject that has fascinated me since it first came to my attention in your podcast interview with Dr. Guyenet. Since then I’ve been reading about the physiological role of fermentable fibers, and have found much scientific support for these ideas.

    For example, check out this study, which found that an experimental group supplemented with resistant starch (a fermentable fiber) extracted from kidney beans lost more fat than a control group, even though both were fed a high-carb diet:


    Recently I began taking psylium husk supplements (1-2 grams) with each meal, and in the past two weeks I’ve averaged over a half-pound of weight loss per day, even though I’ve continued eating carb-heavy foods such fruit, orange juice, and brown rice and haven’t changed my exercise routine. Your readers might try this for themselves.

  45. Hey Chris,

    Since some of the studies you cited found bad effects on gut flora with a high fat diet, would you recommend a low-fat diet as a way to have healthy bacteria?

    • Hi Chris,
      Love your article. One question, do I take probiotics forever or do we take it for a couple of years then give it a break and start again.

  46. Unfortunately, most of the highest quality brands aren’t available directly to consumers.

    For brands you can buy in the store or online, I think Biokult (http://www.bio-kult.com/) is probably one of the best.

    Prebiotics may ultimately be even more important than probiotics in restoring healthy gut flora, but some people don’t tolerate them well. They can cause a lot of gas and bloating, especially if you don’t build up the dose slowly.

    • Hey Chris, my company manufacturers an incredible digestion product that is single serve, powder, probiotic/prebiotic/enzymes. It has made a huge impact on our families health and that of many of my clients. My heart hurts for the mom suffering with her little 7 year old son. I would love to send her some samples with my compliments. It is not remotely about a “sale” for me, but the ability to help this child feel better and thrive. Any chance you can connect us? Thanks for your help!

    • Chris, I was glad to see you also recommend PrescriptAssist soil based probiotic prebiotic. What are your thoughts on taking something like Biocult AND PrescriptAssist? (Starting with fractions of capsule and gradually increasing)

  47. Chris – Any suggestions for high quality probiotics? And what do you think about prebiotics (e.g. fructooligosaccharides) as a potential supporter of gut health? Thanks!

  48. The best choices are primarily starchy tubers like sweet potato, yam, yucca (a.k.a. manioc root), taro and lotus. White potatoes are also okay, but peeled since the skin has toxins and anti-nutrients.

  49. hello. i was wondering if you could list some more fermentable starches. interesting topics dude. i would like to know some more of restoring gut health for my patients after antibiotic use for long term nsaid use.

  50. I wonder if the same could be true for being underweight. My husband has a difficult time keeping weight on. I think he has some digestive issues. Recently his GP said that he might have a Candida problem. Could that be connected to his steady weight loss?

  51. ahhh i love this article…now, if you could focus the big link between the brain-gut regulation i think you’d have a masterpiece…. a lot of what happens in the gut is a by product of the brain and vise versa…nice to see someone isnt focusing on calories and carbs 🙂

  52. Excellent question.

    The sequence goes like this: first remove, then replace, restore and repair.

    It’s important to clear the infection first, because any attempts to repair the gut without doing that will otherwise be ineffective. Once the infection is cleared, the gut flora can be restored with probiotics and prebiotics, or fecal bacteriotherapy.

    • But there are more possibility for the removal of some good microbes with the worst one in the application of antibiotics. will not it hamper the natural microbiota?? And also when we restore the gut with external probiotics, the probability of these external agent’s to be dominated upon the natural microbiota will more!! Will not this be harmful??

  53. Hi Chris,

    How do you deal with the issue that the cure for chronic infections is antibiotics – which is also not good for your gut bacteria. At which point does the cure become worse than the disease its trying to combat?

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